The paper deals with the use of coupled bond graph as an integrated decision tool for health monitoring of chemical reactors. A bond graph model based diagnostic strategy is adopted to detect and isolate kinetic and thermodynamic drift of chemical reactors due to the appearance of secondary reactions. Furthermore, the causal and structural properties of the bond graph model are used not only for system dynamics simulation but also to design Fault Detection and Isolation (FDI) algorithms (i.e. the generation of formal fault indicators) for online supervision of faults affecting sensors, actuators, physico-chemical components and phenomena. (C) 2011 Elsevier Ltd. All rights reserved.